diff variant_effect_predictor/Bio/Symbol/AlphabetI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Symbol/AlphabetI.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,160 @@
+# $Id: AlphabetI.pm,v 1.5 2002/10/22 07:45:21 lapp Exp $
+#
+# BioPerl module for Bio::Symbol::AlphabetI
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Symbol::AlphabetI - A Symbol Alphabet
+
+=head1 SYNOPSIS
+
+    # get a Bio::Symbol::AlphabetI object somehow
+    my @symbols = $alphabet->symbols;
+    my @subalphas = $alphabet->alphabets;
+    if( $alphabet->contains($symbol) ) {
+	# do something
+    }
+
+=head1 DESCRIPTION
+
+Alphabet contains set of symbols, which can be concatenated to form
+symbol lists. Sequence string, for example, is stringified
+representation of the symbol list (tokens of symbols).
+
+This module was implemented for the purposes of meeting the
+BSANE/BioCORBA spec 0.3 only.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+package Bio::Symbol::AlphabetI;
+use strict;
+use Bio::Root::RootI;
+
+=head2 AlphabetI Interface methods
+
+=cut
+
+=head2 symbols
+
+ Title   : symbols
+ Usage   : my @symbols = $alphabet->symbols();
+ Function: Get/Set Symbol list for an alphabet
+           List of symbols, which make up this alphabet.
+ Returns : Array of L<Bio::Symbol::SymbolI> objects
+ Args    : (optional) Array of L<Bio::Symbol::SymbolI> objects
+
+=cut
+
+sub symbols{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 alphabets
+
+ Title   : alphabets
+ Usage   : my @alphabets = $alphabet->alphabets();
+ Function: Get/Set Sub Alphabet list for an alphabet 
+           Sub-alphabets. E.g. codons made from DNAxDNAxDNA alphabets
+ Returns : Array of L<Bio::Symbol::AlphabetI> objects
+ Args    : (optional) Array of L<Bio::Symbol::AlphabetI> objects
+
+=cut
+
+sub alphabets{
+    my ($self,@args) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 contains
+
+ Title   : contains
+ Usage   : if($alphabet->contains($symbol)) { }
+ Function: Tests of Symbol is contained in this alphabet
+ Returns : Boolean
+ Args    : L<Bio::Symbol::SymbolI>
+
+=cut
+
+sub contains{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+# Other methods from BSANE - not sure if we will implement here or only in
+# BioCORBA implementation
+
+# Resolve symbols from the token string.
+#    SymbolList to_symbol(in string tokens) raises ( IllegalSymbolException) ;
+
+# Convinience method, which returns gap symbol that do not
+# match with any other symbols in the alphabet.
+#   Symbol get_gap_symbol() raises ( DoesNotExist) ;
+
+
+# Returns a ambiguity symbol, which represent list of
+# symbols. All symbols in a list must be members of
+# this alphabet otherwise IllegalSymbolException is
+# thrown.
+# Symbol get_ambiguity( in SymbolList symbols) raises( IllegalSymbolException);
+
+
+#  Returns a Symbol, which represents ordered list of symbols
+#  given as a parameter. Each symbol in the list must be member of
+#  different sub-alphabet in the order defined by the alphabets
+#  attribute. For example, codons can be represented by a compound
+#  Alphabet of three DNA Alphabets, in which case the get_symbol(
+#  SymbolList[ a,g,t]) method of the Alphabet returns Symbol for
+#  the codon agt.<p>
+
+#  IllegalSymbolException is raised if members of symbols
+#  are not Symbols over the alphabet defined by
+#  get_alphabets()-method
+#  Symbol get_symbol(in SymbolList symbols) raises(IllegalSymbolException) ;
+
+1;